Each property keyword has different arguments, described below.
Property keywords and their sub-keywords can be truncated
to unique strings, and their case does not matter.
Models are specified by model number preceded by #.
Synonyms for true: True, 1. Synonyms for false: False, 0.
A vertical bar “|” designates mutually exclusive options,
and default settings are indicated with bold.

Calculate the total area of each specified
surface piece
by summing over its triangles. The surface pieces in a
surface model
can be specified collectively by model number, or individually by
selection from the screen
and using the word sel, selected, or picked.
Like Measure
Volume and Area, the calculation uses the full surface even if it is
partly hidden by clipping or zoning.

Note that the solvent-excluded and solvent-accessible surface areas of a
molecular surface
are reported in the Reply Log
when the surface is first shown, and the
values per atom and residue are assigned as
attributes named areaSES and areaSAS, respectively.

Calculate the surface area buried between two
specified sets of atoms.
A surface is calculated for each set of atoms separately (surfA, surfB)
and for their combination (surfAB).
The surfaces are not created or displayed, but calculated internally.
The difference in total area between the separate and combined states is
reported for each set, as well as the average over the two sets.
Buried areas are reported for both
solvent-excluded and solvent-accessible surfaces.
Only the averages are sent to the
status line,
but full results can be viewed in the
Reply Log.

The atoms are grouped as specified regardless of
surface category,
and a set may span multiple models.
Be careful to specify only the intended atoms, which could mean
excluding or deleting beforehand
any solvent, ligands, ions, and/or alternate location atoms.
New Surfaces preference
settings are not used; disjoint surfaces are always included,
and the default probe radius and vertex density are
1.4 Å and 2.0/Å2, respectively.

Atoms are assigned the
attributesburiedSESArea (buried solvent-excluded surface area)
and buriedSASArea (buried solvent-accessible surface area)
with their individual contributions to the specified interface.
These can be summed over selected atoms with
Attribute
Calculator, for example to determine the contribution from carbons only.

To evaluate degree of residue burial in an overall protein structure,
as opposed to a specific interface, it may be helpful
to calculate relative exposure
(a normalized surface area).

Calculate the center of mass of each density map and/or set of atoms
in spec. Map centers are reported in grid indices,
atomic centers of mass in the atomic coordinate system.
The level option indicates using only map regions
above contour-level.
If mark is true, a
marker will be placed at at each computed center, with
radius marker-radius (default based on the contents of spec)
and color marker-color (default gray).
The marker-color can be any
color name that specifies a single color.
The marker model is opened as number model-number
(default next unused number) with name model-name
(default based on the contents of spec).

Report the surface area of one
surface model (surf-model1)
that lies within a cutoff distance of another
surface model (surf-model2).
Unless show false or offset 0 is specified,
a new surface model is created to show the corresponding patch of
surf-model1. The patch-color can be any
color name that specifies a single color
(default red). The new surface can be offset from the
original surf-model1 by a distance d specified in physical units,
typically Å (default 1.0). An offset of zero indicates
recoloring surf-model1 to show the patch
instead of creating a new surface model.
The slab option overrides any offset and
generates a slab of finite thickness instead of a single layer of surface.
If a single value is supplied for the slab width,
its inner and outer layers will be offset
from surf-model1 by ±½(width).
Alternatively, two values separated by a comma but no spaces can be used
to specify the offsets of the two slab layers independently.
Patch or slab offsets can be positive (outward) or negative (inward).
Offsets affect only the display, not the area measurement,
which is taken at the surf-model1 surface.
The smooth option smooths the new surface but is generally
not recommended.
The optimize setting speeds up the calculation
by disregarding far-apart portions of the surfaces.
Currently, each model must contain only a single
surface piece
(it may be necessary to turn off surface capping, see
sop cap).

Calculate the correlation between two volume
data sets (maps) in two ways:

<u,v>

correlation =

|u||v|

<u–uave,v–vave>

correlation about mean =

|u–uave||v–vave|

where vector u contains the values of the first map (map-model1)
and uave is a vector with all components equal to the
average of the components of u. Vectors v and
vave are defined analogously for the second map
(map-model2),
except that the values are sampled at the grid point locations of the
first map using trilinear interpolation.

If aboveThreshold is true (default),
the calculation will include only the grid points in the first map
with values above its lowest contour level in
Volume Viewer.
Otherwise, all nonzero-valued grid points will be included.

Specifying rotationAxis allows calculating the correlation
multiple times for different orientations of the first map about an
axis, described by an
atom-spec of
exactly two atoms (not necessarily bonded or in the same model) or one bond.
If two atoms, the order of specification defines a handedness, and right-handed
rotations are positive. If a bond, the handedness is not under user control.
A bond can only be specified by selecting
it and using the word selected, sel, or picked;
any atoms also selected at the time will be ignored.
The calculations are performed internally, without moving the
map in the display.

The angleRange arguments control how many correlation calculations
should be performed and at what angles of the first map
relative to its current position.
By default, start = 0°, end = 360°,
and step = 2°.

If plot is true (default), the correlation values
will be graphed in a separate window in addition to being tabulated in the
Reply Log. Clicking and dragging in
the plot window will show a vertical line and rotate the first map
to the indicated angle.

Report the closest distance between one set of atoms and/or
surface pieces
(atoms-surfs1) and another set (atoms-surfs2).
Surface models and their pieces can be specified by model number
or as a selection
(details...).
Atoms or surface pieces
belonging to both sets are removed from the second set.
Distances to surfaces are computed to the vertices of the surface mesh.
All surface vertices are considered, even if hidden.
Setting multiple to true gives the closest distance
from each atom and surface piece in the first set
to any in the second set.
Lines depicting the distances can be displayed with show true,
and the line-color can be any
color name
that specifies a single color (default cyan).
The lines are generated as a
surface model.

Calculate electric field lines for one or more
electrostatic potential maps.
The lines option specifies the number N of field lines
to generate per map (default 1000). The lines originate at
grid points with potential magnitudes greater than startAbovecutoff value (default the highest contour level displayed for that map,
or 10 if no contour levels are displayed)
and are traced along the map gradient in steps of s
(default 0.5) times the maximum grid spacing of the map
(details...).
The field lines are added as a new model with ID number model-number
(default next unused number), and the
line-color can be any color name
that specifies a single color (default 0.7,0.7,0.7,1).

The lines will be shown as wires of lineWidthwidth
(default 1) unless a radius for tube display is given
and/or markers is set to true.
In the case of markers true, tubes will be created as a
marker set,
with default radius 0.5 times the maximum grid spacing.
In the case of markers false, the wires or tubes will be created
as a surface model,
with M facets (default 12) used to approximate
the circular cross-section of tubes.
Surface models can subsequently be colored by the potential using
Electrostatic
Surface Coloring or the command scolor.

If the command runs without error but no lines (or few) are visible,
perhaps many short lines not protruding above the surface were generated.
It may be helpful to use a higher startAbove value, and secondarily,
to increase the total number of lines (details...).

Calculate the inertia ellipsoid for
atom-spec, which could
include atoms and/or surface pieces.
Atoms are mass-weighted;
surface pieces are treated
as thin shells with mass proportional to surface area
(details...).
If both atoms and surfaces are specified, two separate ellipsoids are
calculated (a combined calculation cannot be performed).
Principal axes, lengths, moments, and center are reported for each ellipsoid,
using the model coordinate system of the first atom or surface piece
specified to define it.
The vectors v1, v2, and v3 are the principal axes (longest to shortest).
The lengths a, b, c are half-diameters along axes v1, v2, and v3,
respectively. The moments r1, r2, and r3 are calculated as
(inertia/mass)½
about axes v1, v2, and v3, respectively. They can be considered
effective radii; placing all of the mass at that distance from the center
would reproduce the moment of inertia calculated for the structure
around that axis.

The perChain option indicates whether
to calculate a separate ellipsoid for each chain in
atom-spec.
If showEllipsoid is true (default),
the ellipsoid(s) will be opened as a
surface model.
The ellipsoid-color can be any
color name
that specifies a single color. Otherwise, an ellipsoid will be colored
to match the first atom or surface piece in its calculation.

Calculate the mean, standard deviation (SD) from the mean,
and root-mean-square (RMS) deviation from zero for each specified map.
The step option indicates whether to use the full resolution of the
data (step size 1, default) or a specified
subsample (step size > 1). Step sizes must be integers.
A step size of N indicates using every Nth point.
If a single number is supplied, it is
used along all three axes; if three numbers are supplied
(separated by commas but not spaces), they
are used along the X, Y, and Z axes, respectively.
The subregion option indicates whether to use
the full extents of the data (all, default) or a specified
subregion. A subregion can be specified by:

Interpolate map-model to obtain values at the positions of the
atoms in
atom-spec.
The values will be assigned as an atom
attribute,
either named as indicated with name, or (default) derived
by prepending “value_” to the name of map-model and
replacing any non-alphanumeric characters with underscores.
The report option indicates how many values should be reported in the
Reply Log, those for the first N
atoms (default 10, but 0 can be used) or all.

Report the length of the specified bonds.
The group option indicates a single total for all,
or separate totals for bonds within different connected groups
or models, or simply the length of each individual bond.
This measurement applies to
links between markers as well as to standard bonds.

a matrix in which the first three columns describe a rotation
and the fourth describes a translation (performed after the rotation)

an axis of rotation (a unit vector), point on the axis,
rotation angle, and shift parallel to the axis

This command does not evaluate how to best fit or match
the two models. It reports the current rotation and translation
between the coordinate systems of the two models, which would be zero
unless one model was moved relative to the other, either
manually
or with some other tool or command such as
Fit in Map,
match, or
matchmaker.
(Moving everything collectively, such as rotating or zooming to get a better
view, does not change the positions of models relative to each other.)

To get the transformation between
atomic structures that are similar but displaced from one another
(without actually superimposing them),
using the match command with
move false and
showMatrix true
is recommended instead.

The transformation is expressed in the coordinate system of model1
unless a different coordinateSystemN
(model ID number preceded by #) is specified.
If showAxis is true (default), a
marker set showing the axis as a rod
will be opened as a separate model.
The rod length equals the largest dimension of the bounding box
of model1, and its diameter is set to 5% of the length.
If showSlabs is true (default false), two rectangular
slabs showing the rotation axis and angle and the shift will be opened
as a surface model.
The axis and/or slab color can be any
color name that specifies a single color.

Calculate and display a
path along the center line of each specified
segmentation region.
The length of the path (spine) and orthogonal diameters at its midpoint
are reported.
Regions can be specified as a selection (e.g., sel)
or with model number(s) (e.g., #1).
The longest principal axis of inertia of a region is determined
using equal weighting of the enclosed volume grid points.
The region is then divided into slices along that axis,
with end slices tipLengtht thick and
interior slices at least spacings thick.
Both distances are specified in physical units (typically Å).
The default spacings is 20 times the minimum segmentation
grid plane spacing, and the default tipLengtht = 0.2s.
The spacing is increased as needed to make the interior slices of equal width.
A marker is placed at the geometric center of
the grid points within each slice. The markers are linked, and the
markers and links together form a
path. The path color can be any
color name that specifies a single color.
For each pair of consecutive links in the path, the curvature is measured
as 1/r, where r is the radius of a circle tangent to the
midpoints of the links. The minimum, maximum, and average
(weighting each value along the path equally) curvatures are assigned as
segmentation
region attributes named curvature minimum, curvature maximum,
and curvature average, respectively.

Check each specified volume
data set (map) for cyclic, dihedral, tetrahedral, octahedral,
and icosahedral symmetries in standard coordinate systems.
Helical symmetry can be considered if approximate parameters are supplied.
The symmetry assignment can be used by
other commands such as sym
and fitmap, and is included in
Chimera map format.
For direct assignment of a specified symmetry, see the command
volume symmetry.

If the correlation
of the map with itself after symmetry transformation
is at least mincorr (default 0.99), the detected
type of symmetry will be reported, and if set is true,
assigned to the map in Chimera.
The correlation calculation uses only map points with values
above the displayed contour level; if the number of such points exceeds
maxpts (default 10,000), a random sample of maxpts
is chosen from them and used. Values in the first copy of the map
are compared with the superimposed (interpolated) values in the
rotated copy of the map.

Center of point symmetry is considered only at the following:

the grid point nearest the average indices of grid points
with values above the displayed contour level.
The map's lowest contour level in
Volume Viewer is used.

one or two grid points based on the overall map dimensions:
only the midpoint along axes with odd numbers of points, and
along axes with even numbers of points, those on either side of the midpoint.
Rather than all possible combinations for axes with even numbers of points,
only the two points with all indices lower or all higher are evaluated.

For cyclic and dihedral symmetry, rotation is considered only
about the Z axis, and for dihedral symmetry, flipping symmetry only
about the X or Y axes. Cyclic (Cn) symmetry is
checked for order n up to nMax, default 8.
If more than one Cn symmetry meets the criterion,
those for which a higher multiple is also found are discarded, and of
the remaining, the one with the highest correlation is assigned.
For example, if n = 2, 3, 6, and 7 were to meet the criterion,
6-fold would override 2- and 3-fold, and 6-fold or 7-fold symmetry,
whichever gave the highest correlation, would be assigned.
Tetrahedral symmetry is considered in two orientations:

2-folds along X, Y, and Z, with a 3-fold along axis (1,1,1)

3-fold along Z, with a second 3-fold in the YZ plane such that
rotation about the X axis by ~110° is a symmetry operation
(EMAN convention)

Icosahedral symmetries are only considered
in the eight orientations listed in the
Icosahedron
Surface dialog.

The helix option specifies looking for helical symmetry with
approximate rise (in physical units of distance, typically Å)
and angle (degrees) per asymmetric unit. If this option is
used, the other types of symmetry are not considered except for
combined helical and cyclic symmetry (for example,
EMD-1757, approximately
42 Å rise and 21° twist per subunit).
Helical symmetry is infinite, but the number of copies to place
when considering that symmetry, n, is necessarily finite.
If not given, n will be determined by dividing the apparent length of
the helix in the map by the rise and rounding to the nearest positive integer.
The opt keyword indicates optimizing the fit of the map copies to
itself to identify more accurate helical parameters.

Calculate the total volume enclosed by each specified
surface piece,
not including any interior bubbles. The surface pieces in a
surface model
can be specified collectively by model number, or individually by
selection from the screen
and using the word sel, selected, or picked.
Like Measure
Volume and Area, the calculation uses the full surface even if it is
partly hidden by clipping or zoning, and holes are treated as if covered by
planar caps.

TECHNICAL NOTES

Electric field line placement.
A key issue for measure fieldLines is
which lines to compute, out of an infinite number of possibilities.
The basic idea is to make the number of lines originating from a charge
proportional to the magnitude of the charge. This is approximated by
computing the magnitude of the gradient squared divided by the potential
at every grid point and using the grid points with the largest N values for
starting N field lines. The rationale is as follows:
near a point charge, the potential is q/r.
The gradient squared divided by the potential is q/r**3
( = (q/r**2)**2 / (q/r)).
If for a chosen point (gradient squared / potential) > C,
then q/r**3 > C and r**3 < q/C.
The number of grid points around a charge is proportional to the volume r**3,
so is linear in charge.

The resulting field lines can vary greatly
depending on the charge distribution used to compute the potential.
When charges are concentrated on fewer atoms, longer lines are generated,
but when charges are distributed onto many atoms, there may be many
short lines that do not extend beyond the molecular surface.
In that case, it may be helpful to use a higher startAbovecutoff value and a larger number of lines
(total) to get more lines that loop beyond the surface.

I is a 3x3 matrix with indices j and k (j=1,2,3 and k=1,2,3).
Each matrix element is a sum over atoms,
where mi and xi are the mass and position of atom i,
respectively, and δjk is 1 for j=k, otherwise 0.
The principal axes are the eigenvectors of the matrix,
and the moments about those axes are the eigenvalues.
Basically, the moment is a sum of mass times distance squared from the
rotation axis. Before this formula is applied, the center of mass
position is subtracted from the atom coordinates,
so that the measured quantity is the inertia about the center of mass.
The approach for surfaces is analogous, where atoms are replaced
by vertices of the triangulated surface, and the “mass”
of each vertex is &frac13; of the area of the attached triangle.
This treats the surface as a thin shell.
The “inertia ellipsoid” shown by Chimera is not the same
as the one defined in physics. Instead, it is the ellipsoid that has
the same inertia as the measured object:

For atoms, we show the surface of a uniform-density solid ellipsoid
that has the same principal axes and moments as the atoms.

For surfaces, we show an ellipsoidal surface that as a thin shell
has the same axes and moments as the measured surface.